Brain simulation as a cloud service: The Virtual Brain on EBRAINS

The Virtual Brain (TVB) is now available as open-source services on the cloud research platform EBRAINS (ebrains.eu). It offers software for constructing, simulating and analysing brain network models including the TVB simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional brain networks; combined simulation of large-scale brain networks with small-scale spiking networks; automatic conversion of user-specified model equations into fast simulation code; simulation-ready brain models of patients and healthy volunteers; Bayesian parameter optimization in epilepsy patient models; data and software for mouse brain simulation; and extensive educational material. TVB cloud services facilitate reproducible online collaboration and discovery of data assets, models, and software embedded in scalable and secure workflows, a precondition for research on large cohort data sets, better generalizability, and clinical translation

Input to the European Commission stakeholder consultation on the "2015 international climate change agreement: shaping international climate policy beyond 2020" by the Wuppertal Institute for Climate, Environment and Energy : stakeholder input

As part of the discussion on a new international climate agreement, which is supposed to be concluded by 2015, the European Commission conducted a stakeholder consultation, to which the Wuppertal Institute contributed. The Wuppertal Institute suggests that Parties should revisit the widely shared assumption that there is a trade-off between climate protection and economic well-being. The problem is not so much the macro-economic outlook. The problem is that climate policy causes substantial distributional impacts and thus naturally leads to resistance. The Wuppertal Institute recommends to reconsider the political wisdom of the quantity-based approach that climate policy has so far been based on. As long as emissions are seen as inextricably linked to economic well-being, framing commitments in terms of emission reductions directly triggers the perspective of seeing climate protection as an economic loss. Commitments should ideally be multi-dimensional. Possible types of commitments to consider may include scaling up certain climate-friendly technologies, improving energy efficiency, limiting fossil fuel use and fossil fuel extraction, or emission price commitments. The strongest mobilisation of political support might perhaps be achieved by framing commitments as a joint international undertaking to provide universal access to sustainable energy services by a specific date

Integrating neuroinformatics tools in TheVirtualBrain

International audienceTheVirtualBrain (TVB) is a neuroinformatics Python package representing the convergence of clinical, systems, and theoretical neuroscience in the analysis, visualization and modeling of neural and neuroimaging dynamics. TVB is composed of a flexible simulator for neural dynamics measured across scales from local populations to large-scale dynamics measured by electroencephalography (EEG), magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI), and core analytic and visualization functions, all accessible through a web browser user interface. A datatype system modeling neuroscientific data ties together these pieces with persistent data storage, based on a combination of SQL and HDF5. These datatypes combine with adapters allowing TVB to integrate other algorithms or computational systems. TVB provides infrastructure for multiple projects and multiple users, possibly participating under multiple roles. For example, a clinician might import patient data to identify several potential lesion points in the patient's connectome. A modeler, working on the same project, tests these points for viability through whole brain simulation, based on the patient's connectome, and subsequent analysis of dynamical features. TVB also drives research forward: the simulator itself represents the culmination of several simulation frameworks in the modeling literature. The availability of the numerical methods, set of neural mass models and forward solutions allows for the construction of a wide range of brain-scale simulation scenarios. This paper briefly outlines the history and motivation for TVB, describing the framework and simulator, giving usage examples in the web UI and Python scripting

A roadmap to generate renewable protein binders to the human proteome

Despite the wealth of commercially available antibodies to human proteins, research is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein binders. We report a multicenter study to assess the potential of hybridoma and phage-display technologies in a coordinated large-scale antibody generation and validation effort. We produced over 1,000 antibodies targeting 20 SH2 domain proteins and evaluated them for potency and specificity by enzyme-linked immunosorbent assay (ELISA), protein microarray and surface plasmon resonance (SPR). We also tested selected antibodies in immunoprecipitation, immunoblotting and immunofluorescence assays. Our results show that high-affinity, high-specificity renewable antibodies generated by different technologies can be produced quickly and efficiently. We believe that this work serves as a foundation and template for future larger-scale studies to create renewable protein binders